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how to convert gff and fasta file to genbank format

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  • how to convert gff and fasta file to genbank format

    Hi everyone,
    I want convert gff and fasta file to genbank format, is there a software or perl
    script can do this? Waiting for your help. Thank you.

  • #2
    Maybe this thread can help:
    http://seqanswers.com/forums/showthread.php?t=40652

    Comment


    • #3
      Hi TiborNagy,
      Thank you for your reply. I already tried that before,but that is not just what I wanted. That tool can convert gff or fasta to genbank format, but it can not convert gff and fasta to genbank like follows which contains both annotation and sequence.

      LOCUS OB_HTE831 3630528 bp DNA circular BCT 11-DEC-2002
      DEFINITION Oceanobacillus iheyensis HTE831, complete genome.
      ACCESSION
      VERSION
      KEYWORDS .
      SOURCE Oceanobacillus iheyensis HTE831
      ORGANISM Oceanobacillus iheyensis HTE831
      Bacteria; Firmicutes; Bacillales; Oceanobacillus.
      REFERENCE 1 (bases 1 to 3630528)
      AUTHORS Takami,H., Takaki,Y. and Uchiyama,I.
      TITLE Genome sequence of Oceanobacillus iheyensis isolated from the Iheya
      Ridge and its unexpected adaptive capabilities to extreme
      environments
      JOURNAL Nucleic Acids Res. 30 (18), 3927-3935 (2002)
      PUBMED 12235376
      REFERENCE 2 (bases 1 to 3630528)
      AUTHORS Takami,H., Takaki,Y. and Chee,G.
      TITLE Direct Submission
      JOURNAL Submitted (26-DEC-2001) Hideto Takami, Japan Marine Science and
      Technology Center, Deep-sea Microorganisms Research Group; 2-15
      Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
      FEATURES Location/Qualifiers
      source 1..3630528
      /organism="Oceanobacillus iheyensis HTE831"
      /strain="HTE831"
      /db_xref="taxon:221109"
      gene 1830..2966
      /gene="dnaN"
      /locus_tag="OBB_0002"
      CDS 1830..2966
      /gene="dnaN"
      /locus_tag="OBB_0002"
      /EC_number="2.7.7.7"
      /codon_start=1
      /transl_table=11
      /product="DNA-directed DNA polymerase III beta chain"
      /translation="MRFTIQRDKLINGVSNVMKAISARTVIPILTGMKIEVKNHGVTL
      TGSDSDISIEYYIPIEEDGIVHVENIEEGTIILQAKYFPDIVRKLPESTVDIVVDDQL
      NVRITSGKAEFNLNGQSAEEYPQLPKVQTENSFELPIDLLKSMIKQTVFAVSTMETRP
      ILTGVNLKLVDNSLSFTATDSHRLARREIPVSNAPIEISQIVVPGKSLNELNKILGDS
      EETVEISVTNNQILFRTKHLNFLSRLLDGNYPETSRLIPEQSKTKIQLKTKELLGTID
      RASLLAKEERNNVVKFNAPGNSMIEISSNSPEVGNVVEEITADQMEGEDVKISFSSKY
      MIDALKAIEYDEVQIEFTGAMRPFIIRPVGDDSILQLILPVRTY"

      Comment


      • #4
        You can use seqret from emboss.
        Source

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        • #5
          Thank you. I will try it.

          Comment

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